Example usage for java.util TreeSet addAll

Introduction

In this page you can find the example usage for java.util TreeSet addAll.

Prototype

public boolean addAll(Collection<? extends E> c) 

Source Link

Document

Adds all of the elements in the specified collection to this set.

Usage

From source file:com.salesforce.ide.upgrade.ui.wizards.UpgradeComponentConflictsComposite.java

protected void populateTree(Map<String, List<UpgradeConflict>> upgradeConflicts) {
    TreeSet<String> sortedComponentTypes = new TreeSet<String>();
    sortedComponentTypes.addAll(upgradeConflicts.keySet());

    // loop thru sorted list creating upgrade component tree
    for (String componentType : sortedComponentTypes) {
        // create root component type node
        TreeItem componentTypeTreeItem = new TreeItem(getTreeComponentConflicts(), SWT.NONE);
        componentTypeTreeItem.setText(componentType);
        FontRegistry registry = new FontRegistry();
        Font boldFont = registry.getBold(Display.getCurrent().getSystemFont().getFontData()[0].getName());

        componentTypeTreeItem.setFont(boldFont);
        componentTypeTreeItem.setExpanded(true);

        // loop thru each component instance and create named node
        List<UpgradeConflict> upgradeComponents = upgradeConflicts.get(componentType);
        for (UpgradeConflict upgradeConflict : upgradeComponents) {
            TreeItem componentTreeItem = new TreeItem(componentTypeTreeItem, SWT.NONE);
            componentTreeItem.setText(upgradeConflict.getLocalComponent().getFileName());
            componentTreeItem.setForeground(Display.getCurrent().getSystemColor(SWT.COLOR_BLUE));
            componentTreeItem.setData("local", upgradeConflict.getLocalComponent());
            componentTreeItem.setData("remote", upgradeConflict.getRemoteComponent());
            componentTreeItem.setExpanded(true);
        }//from   w  ww.jav  a  2  s. co  m
    }
}

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From source file:org.openanzo.client.cli.RdfIOCommand.java

Collection<File> getFiles(File dir, boolean recurse) {
    TreeSet<File> files = new TreeSet<File>();
    for (File file : dir.listFiles()) {
        if (file.isDirectory()) {
            if (recurse) {
                files.addAll(getFiles(file, recurse));
            }/*from   w  w  w. j a v  a 2s .  c  o  m*/
        } else {
            files.add(file);
        }
    }
    return files;
}

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From source file:org.openmrs.module.clinicalsummary.rule.antenatal.grouped.DatetimeBasedConceptFilteredRule.java

/**
 * @see org.openmrs.logic.Rule#eval(org.openmrs.logic.LogicContext, Integer, java.util.Map)
 *///from   w  w  w  . ja v a2  s. c  om
@Override
protected Result evaluate(final LogicContext context, final Integer patientId,
        final Map<String, Object> parameters) {
    Result result = new Result();

    Object conceptObjects = parameters.get(EvaluableConstants.OBS_CONCEPT);
    Map<Concept, Integer> conceptNamePositions = searchPositions(conceptObjects);

    ObsWithRestrictionRule obsWithRestrictionRule = new ObsWithStringRestrictionRule();
    Result obsResults = obsWithRestrictionRule.eval(context, patientId, parameters);

    Map<Date, Result[]> obsResultDates = new HashMap<Date, Result[]>();
    for (Result obsResult : obsResults) {
        Obs obs = (Obs) obsResult.getResultObject();
        Date obsDatetime = obs.getObsDatetime();
        // see if we already have obs array for this date
        Result[] obsResultDate = obsResultDates.get(obsDatetime);
        if (obsResultDate == null) {
            obsResultDate = new Result[CollectionUtils.size(conceptNamePositions)];
            obsResultDates.put(obsDatetime, obsResultDate);
        }
        // search the concept in the concept ordering map
        Integer position = conceptNamePositions.get(obs.getConcept());
        if (position != null)
            obsResultDate[position] = obsResult;
    }

    TreeSet<Date> keys = new TreeSet<Date>(new Comparator<Date>() {

        public int compare(final Date firstDate, final Date secondDate) {
            return firstDate.equals(secondDate) ? 0 : firstDate.after(secondDate) ? -1 : 1;
        }
    });
    keys.addAll(obsResultDates.keySet());

    // TODO: need to merge the two loop into one
    Integer counter = 0;
    Iterator<Date> iterator = keys.iterator();
    while (iterator.hasNext() && counter < 5) {
        Date date = iterator.next();
        // create the grouped results
        Result groupedResult = new Result();
        groupedResult.add(new Result(date));
        groupedResult.addAll(Arrays.asList(obsResultDates.get(date)));
        // add them to the main result of the rule
        result.add(groupedResult);
        // increase the counter as we only want last 5
        counter++;
    }

    Collections.reverse(result);

    return result;
}

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From source file:net.spfbl.core.Peer.java

public synchronized static TreeSet<Peer> getSet() {
    TreeSet<Peer> peerSet = new TreeSet<Peer>();
    peerSet.addAll(MAP.values());
    return peerSet;
}

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From source file:evaluation.Evaluator.java

/**
 * This function removes duplicates from an array of given labels. It is used while
 * reading the file with the predicted labels.
 *
 * @param labels    the array with the labels to be checked for duplicates
 *///from   w w w . j a v  a 2s .c  o  m
public String[] removeDuplicates(String labels[]) {
    TreeSet aset = new TreeSet();
    aset.addAll(Arrays.asList(labels));

    int num_of_labels = aset.size();

    String finallabels[] = new String[num_of_labels];
    Iterator iterator = aset.iterator();
    int k = 0;
    while (iterator.hasNext()) {
        finallabels[k++] = (String) iterator.next();
    }

    return finallabels;
}

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From source file:edu.mbl.jif.imaging.mmtiff.FileSet.java

/**
 * Completes the current time point of an aborted acquisition with blank images, so that it can
 * be opened correctly by ImageJ/BioForamts
 *//*  w ww  . j  a  v  a  2  s  . co m*/
private void completeFrameWithBlankImages(int frame) throws JSONException, MMScriptException {

    int numFrames = MDUtils.getNumFrames(mpTiff_.summaryMetadata_);
    int numSlices = MDUtils.getNumSlices(mpTiff_.summaryMetadata_);
    int numChannels = MDUtils.getNumChannels(mpTiff_.summaryMetadata_);
    if (numFrames > frame + 1) {
        TreeSet<String> writtenImages = new TreeSet<String>();
        for (MultipageTiffWriter w : tiffWriters_) {
            writtenImages.addAll(w.getIndexMap().keySet());
            w.setAbortedNumFrames(frame + 1);
        }
        int positionIndex = MDUtils.getIndices(writtenImages.first())[3];
        if (mpTiff_.omeTiff_) {
            mpTiff_.omeMetadata_.setNumFrames(positionIndex, frame + 1);
        }
        TreeSet<String> lastFrameLabels = new TreeSet<String>();
        for (int c = 0; c < numChannels; c++) {
            for (int z = 0; z < numSlices; z++) {
                lastFrameLabels.add(MDUtils.generateLabel(c, z, frame, positionIndex));
            }
        }
        lastFrameLabels.removeAll(writtenImages);
        try {
            for (String label : lastFrameLabels) {
                tiffWriters_.getLast().writeBlankImage(label);
                if (mpTiff_.omeTiff_) {
                    JSONObject dummyTags = new JSONObject();
                    int channel = Integer.parseInt(label.split("_")[0]);
                    int slice = Integer.parseInt(label.split("_")[1]);
                    MDUtils.setChannelIndex(dummyTags, channel);
                    MDUtils.setFrameIndex(dummyTags, frame);
                    MDUtils.setSliceIndex(dummyTags, slice);
                    mpTiff_.omeMetadata_.addImageTagsToOME(dummyTags, ifdCount_, baseFilename_,
                            currentTiffFilename_);
                }
            }
        } catch (IOException ex) {
            ReportingUtils.logError("problem writing dummy image");
        }
    }
}

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From source file:org.jactr.modules.pm.visual.AbstractVisualModule.java

/**
 * Return list of all parameters that can be set.
 * //  www  .j a  va 2 s.  co  m
 * @return The setableParameters value
 */
@Override
public Collection<String> getSetableParameters() {
    TreeSet<String> params = new TreeSet<String>(_parameterMap.keySet());
    params.addAll(SETABLE_PARAMS);
    params.addAll(super.getSetableParameters());
    return params;
}

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From source file:ca.uhn.fhir.rest.server.provider.dev.ServerConformanceProvider.java

private void handleDynamicSearchMethodBinding(RestResource resource, RuntimeResourceDefinition def,
        TreeSet<String> includes, DynamicSearchMethodBinding searchMethodBinding) {
    includes.addAll(searchMethodBinding.getIncludes());

    List<RuntimeSearchParam> searchParameters = new ArrayList<RuntimeSearchParam>();
    searchParameters.addAll(searchMethodBinding.getSearchParams());
    sortRuntimeSearchParameters(searchParameters);

    if (!searchParameters.isEmpty()) {

        for (RuntimeSearchParam nextParameter : searchParameters) {

            String nextParamName = nextParameter.getName();

            // String chain = null;
            String nextParamUnchainedName = nextParamName;
            if (nextParamName.contains(".")) {
                // chain = nextParamName.substring(nextParamName.indexOf('.') + 1);
                nextParamUnchainedName = nextParamName.substring(0, nextParamName.indexOf('.'));
            }/*from   w  w  w. ja  va2s .c om*/

            String nextParamDescription = nextParameter.getDescription();

            /*
             * If the parameter has no description, default to the one from the resource
             */
            if (StringUtils.isBlank(nextParamDescription)) {
                RuntimeSearchParam paramDef = def.getSearchParam(nextParamUnchainedName);
                if (paramDef != null) {
                    nextParamDescription = paramDef.getDescription();
                }
            }

            RestResourceSearchParam param;
            param = resource.addSearchParam();

            param.setName(nextParamName);
            // if (StringUtils.isNotBlank(chain)) {
            // param.addChain(chain);
            // }
            param.setDocumentation(nextParamDescription);
            //            param.setType(nextParameter.getParamType());
        }
    }
}

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From source file:com.kelveden.rastajax.representation.flat.FlatRepresentationBuilder.java

@Override
public Set<FlatResource> buildRepresentationFor(final Set<ResourceClass> resourceClasses) {

    final TreeSet<FlatResource> result = new TreeSet<FlatResource>(RESOURCE_COMPARATOR);

    for (ResourceClass rawResource : resourceClasses) {
        result.addAll(buildRepresentationFor(rawResource));
    }// w w  w.j  a va 2 s . co  m

    LOGGER.info("Representation completed with {} resources.", result.size());

    return result;
}

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From source file:org.broadinstitute.sting.gatk.walkers.variantrecalibration.ApplyRecalibration.java

public void initialize() {
    if (TS_FILTER_LEVEL != null) {
        for (final Tranche t : Tranche.readTranches(TRANCHES_FILE)) {
            if (t.ts >= TS_FILTER_LEVEL) {
                tranches.add(t);//from ww  w  . ja v a 2  s  .  com
            }
            logger.info(String.format("Read tranche " + t));
        }
        Collections.reverse(tranches); // this algorithm wants the tranches ordered from best (lowest truth sensitivity) to worst (highest truth sensitivity)
    }

    for (final RodBinding rod : input) {
        inputNames.add(rod.getName());
    }

    if (IGNORE_INPUT_FILTERS != null) {
        ignoreInputFilterSet.addAll(Arrays.asList(IGNORE_INPUT_FILTERS));
    }

    // setup the header fields
    final Set<VCFHeaderLine> hInfo = new HashSet<>();
    hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames));
    addVQSRStandardHeaderLines(hInfo);
    final TreeSet<String> samples = new TreeSet<>();
    samples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames));

    if (TS_FILTER_LEVEL != null) {
        // if the user specifies both ts_filter_level and lodCutoff then throw a user error
        if (VQSLOD_CUTOFF != null) {
            throw new UserException(
                    "Arguments --ts_filter_level and --lodCutoff are mutually exclusive. Please only specify one option.");
        }

        if (tranches.size() >= 2) {
            for (int iii = 0; iii < tranches.size() - 1; iii++) {
                final Tranche t = tranches.get(iii);
                hInfo.add(new VCFFilterHeaderLine(t.name,
                        String.format("Truth sensitivity tranche level for " + t.model.toString()
                                + " model at VQS Lod: " + t.minVQSLod + " <= x < "
                                + tranches.get(iii + 1).minVQSLod)));
            }
        }
        if (tranches.size() >= 1) {
            hInfo.add(new VCFFilterHeaderLine(tranches.get(0).name + "+",
                    String.format("Truth sensitivity tranche level for " + tranches.get(0).model.toString()
                            + " model at VQS Lod < " + tranches.get(0).minVQSLod)));
        } else {
            throw new UserException(
                    "No tranches were found in the file or were above the truth sensitivity filter level "
                            + TS_FILTER_LEVEL);
        }

        logger.info("Keeping all variants in tranche " + tranches.get(tranches.size() - 1));
    } else {
        if (VQSLOD_CUTOFF == null) {
            VQSLOD_CUTOFF = DEFAULT_VQSLOD_CUTOFF;
        }
        hInfo.add(new VCFFilterHeaderLine(LOW_VQSLOD_FILTER_NAME, "VQSLOD < " + VQSLOD_CUTOFF));
        logger.info("Keeping all variants with VQSLOD >= " + VQSLOD_CUTOFF);
    }

    final VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
    vcfWriter.writeHeader(vcfHeader);
}

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